From 77d73c1194625fe12c6e3f3431b37459e5592d8a Mon Sep 17 00:00:00 2001 From: Renia Correya Date: Fri, 8 Mar 2024 09:16:44 +0000 Subject: [PATCH] JAL-4386 Calculate tree using secondary structure annotation --- .../analysis/scoremodels/FeatureDistanceModel.java | 7 + src/jalview/analysis/scoremodels/PIDModel.java | 6 + src/jalview/analysis/scoremodels/ScoreMatrix.java | 6 + src/jalview/analysis/scoremodels/ScoreModels.java | 4 +- .../SecondaryStructureDistanceModel.java | 306 +++++++++++++++ .../analysis/scoremodels/SmithWatermanModel.java | 6 + src/jalview/api/analysis/ScoreModelI.java | 11 + .../SecondaryStructureDistanceModelTest.java | 397 ++++++++++++++++++++ 8 files changed, 742 insertions(+), 1 deletion(-) create mode 100644 src/jalview/analysis/scoremodels/SecondaryStructureDistanceModel.java create mode 100644 test/jalview/analysis/scoremodels/SecondaryStructureDistanceModelTest.java diff --git a/src/jalview/analysis/scoremodels/FeatureDistanceModel.java b/src/jalview/analysis/scoremodels/FeatureDistanceModel.java index bcc0855..604893c 100644 --- a/src/jalview/analysis/scoremodels/FeatureDistanceModel.java +++ b/src/jalview/analysis/scoremodels/FeatureDistanceModel.java @@ -236,6 +236,13 @@ public class FeatureDistanceModel extends DistanceScoreModel { return true; } + + @Override + public boolean isSecondaryStructure() + { + return false; + } + @Override public String toString() diff --git a/src/jalview/analysis/scoremodels/PIDModel.java b/src/jalview/analysis/scoremodels/PIDModel.java index ddfe5e4..267ef89 100644 --- a/src/jalview/analysis/scoremodels/PIDModel.java +++ b/src/jalview/analysis/scoremodels/PIDModel.java @@ -73,6 +73,12 @@ public class PIDModel extends SimilarityScoreModel { return true; } + + @Override + public boolean isSecondaryStructure() + { + return false; + } /** * Answers 1 if c and d are the same residue (ignoring case), and not gap diff --git a/src/jalview/analysis/scoremodels/ScoreMatrix.java b/src/jalview/analysis/scoremodels/ScoreMatrix.java index aa841ac..a1ea35a 100644 --- a/src/jalview/analysis/scoremodels/ScoreMatrix.java +++ b/src/jalview/analysis/scoremodels/ScoreMatrix.java @@ -280,6 +280,12 @@ public class ScoreMatrix extends SimilarityScoreModel { return peptide; } + + @Override + public boolean isSecondaryStructure() + { + return false; + } /** * Returns a copy of the score matrix as used in getPairwiseScore. If using diff --git a/src/jalview/analysis/scoremodels/ScoreModels.java b/src/jalview/analysis/scoremodels/ScoreModels.java index d9648ba..dd1bc9d 100644 --- a/src/jalview/analysis/scoremodels/ScoreModels.java +++ b/src/jalview/analysis/scoremodels/ScoreModels.java @@ -68,7 +68,8 @@ public class ScoreModels *
  • PAM250
    • *
  • PID
    • *
  • DNA
    • - *
  • Sequence Feature Similarity
    • + *
  • Sequence Feature Similarity
    • * + *
  • Secondary Structure Similarity
    • * */ private ScoreModels() @@ -82,6 +83,7 @@ public class ScoreModels DNA = loadScoreMatrix("scoreModel/dna.scm"); registerScoreModel(new PIDModel()); registerScoreModel(new FeatureDistanceModel()); + registerScoreModel(new SecondaryStructureDistanceModel()); } /** diff --git a/src/jalview/analysis/scoremodels/SecondaryStructureDistanceModel.java b/src/jalview/analysis/scoremodels/SecondaryStructureDistanceModel.java new file mode 100644 index 0000000..7fcee35 --- /dev/null +++ b/src/jalview/analysis/scoremodels/SecondaryStructureDistanceModel.java @@ -0,0 +1,306 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ +package jalview.analysis.scoremodels; + +import jalview.api.AlignmentViewPanel; +import jalview.api.FeatureRenderer; +import jalview.api.analysis.ScoreModelI; +import jalview.api.analysis.SimilarityParamsI; +import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.AlignmentView; +import jalview.datamodel.Annotation; +import jalview.datamodel.SeqCigar; +import jalview.math.Matrix; +import jalview.math.MatrixI; +import jalview.util.SetUtils; + +import java.util.HashSet; +import java.util.Set; + +/* This class contains methods to calculate distance score between + * secondary structure annotations of the sequences. The inverse of + * the score is later calculated for similarity score. + */ +public class SecondaryStructureDistanceModel extends DistanceScoreModel +{ + private static final String NAME = "Secondary Structure Similarity"; + + private String description; + + FeatureRenderer fr; + + /** + * Constructor + */ + public SecondaryStructureDistanceModel() + { + + } + + @Override + public ScoreModelI getInstance(AlignmentViewPanel view) + { + SecondaryStructureDistanceModel instance; + try + { + instance = this.getClass().getDeclaredConstructor().newInstance(); + instance.configureFromAlignmentView(view); + return instance; + } catch (InstantiationException | IllegalAccessException e) + { + jalview.bin.Console.errPrintln("Error in " + getClass().getName() + + ".getInstance(): " + e.getMessage()); + return null; + } catch (ReflectiveOperationException roe) + { + return null; + } + } + + boolean configureFromAlignmentView(AlignmentViewPanel view) + + { + fr = view.cloneFeatureRenderer(); + return true; + } + + /** + * Calculates a distance measure [i][j] between each pair of sequences as the + * average number of features they have but do not share. That is, find the + * features each sequence pair has at each column, ignore feature types they + * have in common, and count the rest. The totals are normalised by the number + * of columns processed. + *

    + * The parameters argument provides settings for treatment of gap-residue + * aligned positions, and whether the score is over the longer or shorter of + * each pair of sequences + * + * @param seqData + * @param params + */ + + /** + * Calculates distance score [i][j] between each pair of protein sequences + * based on their secondary structure annotations (H, E, C). That is, find the + * secondary structures each sequence has at each column and scores positively for + * each non similar secondary structure annotations. Scores 0 for similar secondary + * structure annotations. The final score is normalized by the number of + * alignment columns processed, providing an average similarity score. + *

    + * The parameters argument can include settings for handling gap-residue aligned + * positions and may determine if the score calculation is based on the longer or shorter + * sequence in each pair. This can be important for handling partial alignments or + * sequences of significantly different lengths. + * + * @param seqData The aligned sequence data including secondary structure annotations. + * @param params Additional parameters for customizing the scoring process, such as gap + * handling and sequence length consideration. + */ + @Override + public MatrixI findDistances(AlignmentView seqData, + SimilarityParamsI params) + { + SeqCigar[] seqs = seqData.getSequences(); + int noseqs = seqs.length; //no of sequences + int cpwidth = 0; // = seqData.getWidth(); + double[][] distances = new double[noseqs][noseqs]; //matrix to store distance score + + // need to get real position for view position + int[] viscont = seqData.getVisibleContigs(); + + /* + * scan each column, compute and add to each distance[i, j] + * the number of secondary structure annotation that seqi + * and seqj do not share + */ + for (int vc = 0; vc < viscont.length; vc += 2) + { + //Iterates for each column position + for (int cpos = viscont[vc]; cpos <= viscont[vc + 1]; cpos++) + { + cpwidth++; //used to normalise the distance score + + /* + * get set of sequences without gap in the current column + */ + Set seqsWithoutGapAtCol = findSeqsWithoutGapAtColumn(seqs, cpos); + + /* + * count score for each dissimilar secondary structure annotation on i'th and j'th + * sequence. Igonre if similar and add this 'distance' measure to the total + * for [i, j] for j > i + */ + for (int i = 0; i < (noseqs - 1); i++) + { + //Iterates for each sequences + for (int j = i + 1; j < noseqs; j++) + { + SeqCigar sc1 = seqs[i]; + SeqCigar sc2 = seqs[j]; + boolean gap1 = !seqsWithoutGapAtCol.contains(sc1); + boolean gap2 = !seqsWithoutGapAtCol.contains(sc2); + + //Variable to store secondary structure at the current column + Set secondaryStructure1 = new HashSet(); + Set secondaryStructure2 = new HashSet(); + + //secondary structure is fetched only if the current column is not + //gap for the sequence + if(!gap1) { + secondaryStructure1.addAll( + findSSAnnotationForGivenSeqAndCol(seqs[i], cpos)); + } + + if(!gap2) { + secondaryStructure2.addAll( + findSSAnnotationForGivenSeqAndCol(seqs[j], cpos)); + } + + /* + * gap-gap always scores zero + * residue-residue is always scored + * include gap-residue score if params say to do so + */ + if ((!gap1 && !gap2) || params.includeGaps()) + { + int seqDistance = SetUtils.countDisjunction( + secondaryStructure1, secondaryStructure2); + distances[i][j] += seqDistance; + } + } + } + } + } + + /* + * normalise the distance scores (summed over columns) by the + * number of visible columns used in the calculation + * and fill in the bottom half of the matrix + */ + // TODO JAL-2424 cpwidth may be out by 1 - affects scores but not tree shape + for (int i = 0; i < noseqs; i++) + { + for (int j = i + 1; j < noseqs; j++) + { + distances[i][j] /= cpwidth; + distances[j][i] = distances[i][j]; + } + } + return new Matrix(distances); + } + + /** + * Builds and returns a set containing sequences (SeqCigar) which do not + * have a gap at the given column position. + * + * @param seqs + * @param columnPosition + * (0..) + * @return + */ + protected Set findSeqsWithoutGapAtColumn( + SeqCigar[] seqs, int columnPosition) + { + Set seqsWithoutGapAtCol = new HashSet<>(); + for (SeqCigar seq : seqs) + { + int spos = seq.findPosition(columnPosition); + if (spos != -1) + { + /* + * position is not a gap + */ + seqsWithoutGapAtCol.add(seq); + } + } + return seqsWithoutGapAtCol; + } + + /** + * Finds secondary structure annotation for a given sequence (SeqCigar) + * and column position corresponding to the sequence. + * + * @param seq + * @param columnPosition + * (0..) + * @return + */ + private Set findSSAnnotationForGivenSeqAndCol( + SeqCigar seq, int columnPosition) + { + Set secondaryStructure = new HashSet(); + + char ss = '\0'; //default null character + + //fetch the position in sequence for the column and finds the + //corresponding secondary structure annotation + int seqPosition = seq.findPosition(columnPosition); + AlignmentAnnotation[] aa = seq.getRefSeq().getAnnotation("Secondary Structure"); + if (aa != null) { + Annotation a = aa[0].getAnnotationForPosition(seqPosition); + ss = a.secondaryStructure; + if (ss == ' ') { + ss = 'C'; // In JalView, 'C' is represented as ' ' + } + if (ss != '\0') { // Check if ss is not the default null character + secondaryStructure.add(String.valueOf(ss)); + } + } + return secondaryStructure; + } + + + @Override + public String getName() + { + return NAME; + } + + @Override + public String getDescription() + { + return description; + } + + @Override + public boolean isDNA() + { + return false; + } + + @Override + public boolean isProtein() + { + return false; + } + + @Override + public boolean isSecondaryStructure() + { + return true; + } + + @Override + public String toString() + { + return "Score between sequences based on hamming distance between binary vectors marking features displayed at each column"; + } +} \ No newline at end of file diff --git a/src/jalview/analysis/scoremodels/SmithWatermanModel.java b/src/jalview/analysis/scoremodels/SmithWatermanModel.java index ca6d279..926781a 100644 --- a/src/jalview/analysis/scoremodels/SmithWatermanModel.java +++ b/src/jalview/analysis/scoremodels/SmithWatermanModel.java @@ -96,6 +96,12 @@ public class SmithWatermanModel extends SimilarityScoreModel { return true; } + + @Override + public boolean isSecondaryStructure() + { + return false; + } @Override public String getDescription() diff --git a/src/jalview/api/analysis/ScoreModelI.java b/src/jalview/api/analysis/ScoreModelI.java index 275cd92..97920e5 100644 --- a/src/jalview/api/analysis/ScoreModelI.java +++ b/src/jalview/api/analysis/ScoreModelI.java @@ -62,6 +62,17 @@ public interface ScoreModelI // TODO getName, isDNA, isProtein can be static methods in Java 8 + + boolean isSecondaryStructure(); + + /** + * Answers true if the data has secondary structure (so should be + * shown in menus in that context) + * + * @return + */ + + /** * Returns a distance score for the given sequence regions, that is, a matrix * whose value [i][j] is the distance of sequence i from sequence j by some diff --git a/test/jalview/analysis/scoremodels/SecondaryStructureDistanceModelTest.java b/test/jalview/analysis/scoremodels/SecondaryStructureDistanceModelTest.java new file mode 100644 index 0000000..7da8c65 --- /dev/null +++ b/test/jalview/analysis/scoremodels/SecondaryStructureDistanceModelTest.java @@ -0,0 +1,397 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ +package jalview.analysis.scoremodels; + +import static org.testng.Assert.assertEquals; +import static org.testng.Assert.assertTrue; + +import jalview.api.analysis.ScoreModelI; +import jalview.api.analysis.SimilarityParamsI; +import jalview.datamodel.Alignment; +import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.AlignmentView; +import jalview.datamodel.Annotation; +import jalview.datamodel.Sequence; +import jalview.datamodel.SequenceFeature; +import jalview.datamodel.SequenceI; +import jalview.gui.AlignFrame; +import jalview.gui.AlignViewport; +import jalview.gui.JvOptionPane; +import jalview.io.DataSourceType; +import jalview.io.FileLoader; +import jalview.math.MatrixI; + +import org.testng.Assert; +import org.testng.annotations.BeforeClass; +import org.testng.annotations.Test; + +// This class tests methods in Class SecondaryStructureDistanceModel +public class SecondaryStructureDistanceModelTest +{ + + @BeforeClass(alwaysRun = true) + public void setUpJvOptionPane() + { + JvOptionPane.setInteractiveMode(false); + JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); + } + + public static String alntestFile = "FER1_MESCR/72-76 DVYIL\nFER1_SPIOL/71-75 DVYIL\nFER3_RAPSA/21-25 DVYVL\nFER1_MAIZE/73-77 DVYIL\n"; + + int[] sf1 = new int[] { 74, 74, 73, 73, 23, 23, -1, -1 }; + + int[] sf2 = new int[] { -1, -1, 74, 75, -1, -1, 76, 77 }; + + int[] sf3 = new int[] { -1, -1, -1, -1, -1, -1, 76, 77 }; + + /** + * 

    +   * Load test alignment and add features to sequences: 
+   *      FER1_MESCR FER1_SPIOL FER3_RAPSA FER1_MAIZE 
+   *  sf1     X          X          X  
+   *  sf2                X                     X 
+   *  sf3                                      X
+   *
    + * + * @return + */ + public AlignFrame getTestAlignmentFrame() + { + AlignFrame alf = new FileLoader(false) + .LoadFileWaitTillLoaded(alntestFile, DataSourceType.PASTE); + AlignmentI al = alf.getViewport().getAlignment(); + Assert.assertEquals(al.getHeight(), 4); + Assert.assertEquals(al.getWidth(), 5); + for (int i = 0; i < 4; i++) + { + SequenceI ds = al.getSequenceAt(i).getDatasetSequence(); + if (sf1[i * 2] > 0) + { + ds.addSequenceFeature(new SequenceFeature("sf1", "sf1", sf1[i * 2], + sf1[i * 2 + 1], "sf1")); + } + if (sf2[i * 2] > 0) + { + ds.addSequenceFeature(new SequenceFeature("sf2", "sf2", sf2[i * 2], + sf2[i * 2 + 1], "sf2")); + } + if (sf3[i * 2] > 0) + { + ds.addSequenceFeature(new SequenceFeature("sf3", "sf3", sf3[i * 2], + sf3[i * 2 + 1], "sf3")); + } + } + alf.setShowSeqFeatures(true); + alf.getFeatureRenderer().setVisible("sf1"); + alf.getFeatureRenderer().setVisible("sf2"); + alf.getFeatureRenderer().setVisible("sf3"); + alf.getFeatureRenderer().findAllFeatures(true); + Assert.assertEquals( + alf.getFeatureRenderer().getDisplayedFeatureTypes().size(), 3, + "Number of feature types"); + assertTrue(alf.getCurrentView().areFeaturesDisplayed()); + return alf; + } + + + + /** + * Verify computed distances of sequences with similar secondary structures + */ + @Test(groups = "Functional") + public void testFindDistances_AllSimilar() + { + AlignFrame af = setupAlignmentView("All Similar"); + AlignViewport viewport = af.getViewport(); + AlignmentView view = viewport.getAlignmentView(false); + + ScoreModelI sm = new SecondaryStructureDistanceModel(); + sm = ScoreModels.getInstance().getScoreModel(sm.getName(), + af.alignPanel); + + /* + * feature distance model always normalises by region width + */ + + SimilarityParamsI params = new SimilarityParams(false, true, true, true); + MatrixI distances = sm.findDistances(view, params); + assertEquals(distances.getValue(0, 0), 0d); + assertEquals(distances.getValue(1, 1), 0d); + assertEquals(distances.getValue(0, 1), 0d / 4); + assertEquals(distances.getValue(1, 0), 0d / 4); + } + + /** + * Verify computed distances of sequences with partially similar secondary structures + */ + @Test(groups = "Functional") + public void testFindDistances_PartiallySimilar() + { + AlignFrame af = setupAlignmentView("Partially Similar"); + AlignViewport viewport = af.getViewport(); + AlignmentView view = viewport.getAlignmentView(false); + + ScoreModelI sm = new SecondaryStructureDistanceModel(); + sm = ScoreModels.getInstance().getScoreModel(sm.getName(), + af.alignPanel); + + /* + * score = 0 + 0 + 2 + 2 = 4/4 + */ + SimilarityParamsI params = new SimilarityParams(false, true, true, true); + MatrixI distances = sm.findDistances(view, params); + assertEquals(distances.getValue(0, 0), 0d); + assertEquals(distances.getValue(1, 1), 0d); + assertEquals(distances.getValue(0, 1), 1d); // should be 13d/6 + assertEquals(distances.getValue(1, 0), 1d); + } + + /** + * Verify computed distances of sequences with dissimilar secondary structures + */ + @Test(groups = "Functional") + public void testFindDistances_notSimilar() + { + AlignFrame af = setupAlignmentView("Not Similar"); + AlignViewport viewport = af.getViewport(); + AlignmentView view = viewport.getAlignmentView(false); + + ScoreModelI sm = new SecondaryStructureDistanceModel(); + sm = ScoreModels.getInstance().getScoreModel(sm.getName(), + af.alignPanel); + + /* + * score = 2 + 2 + 2 + 2 = 8/4 + */ + SimilarityParamsI params = new SimilarityParams(false, true, true, true); + MatrixI distances = sm.findDistances(view, params); + assertEquals(distances.getValue(0, 0), 0d); + assertEquals(distances.getValue(1, 1), 0d); + assertEquals(distances.getValue(0, 1), 2d); + assertEquals(distances.getValue(1, 0), 2d); + } + + /** + * Verify computed distances of sequences with gap + */ + @Test(groups = "Functional") + public void testFindDistances_withGap() + { + AlignFrame af = setupAlignmentViewWithGap("Not Similar"); + AlignViewport viewport = af.getViewport(); + AlignmentView view = viewport.getAlignmentView(false); + + ScoreModelI sm = new SecondaryStructureDistanceModel(); + sm = ScoreModels.getInstance().getScoreModel(sm.getName(), + af.alignPanel); + + /* + * feature distance model always normalises by region width + * gap-gap is always included (but scores zero) + * the only variable parameter is 'includeGaps' + */ + + /* + * include gaps + * score = 0 + 0 + 1 + 0 = 1/4 + */ + SimilarityParamsI params = new SimilarityParams(false, true, true, true); + MatrixI distances = sm.findDistances(view, params); + assertEquals(distances.getValue(0, 0), 0d); + assertEquals(distances.getValue(1, 1), 0d); + assertEquals(distances.getValue(0, 1), 1d/4); + assertEquals(distances.getValue(1, 0), 1d/4); + + /* + * exclude gaps + * score = 0 + 0 + 0 + 0 = 0/4 + */ + + SimilarityParamsI params2 = new SimilarityParams(false, true, false, true); + MatrixI distances2 = sm.findDistances(view, params2); + assertEquals(distances2.getValue(0, 1), 0d); + assertEquals(distances2.getValue(1, 0), 0d); + } + + + + /** + * 
    +   * Set up
+   *   column      1 2 3 4 
+   *        seq s1 F R K S
+   *        
+   *        seq s2 F S J L
+   *
    + * + * @return + */ + protected AlignFrame setupAlignmentView(String similar) + { + /* + * sequences without gaps + */ + SequenceI s1 = new Sequence("s1", "FRKS"); + SequenceI s2 = new Sequence("s2", "FSJL"); + + s1.addSequenceFeature( + new SequenceFeature("chain", null, 1, 4, 0f, null)); + s1.addSequenceFeature( + new SequenceFeature("domain", null, 1, 4, 0f, null)); + s2.addSequenceFeature( + new SequenceFeature("chain", null, 1, 4, 0f, null)); + s2.addSequenceFeature( + new SequenceFeature("metal", null, 1, 4, 0f, null)); + s2.addSequenceFeature( + new SequenceFeature("Pfam", null, 1, 4, 0f, null)); + + + /* + * Set up secondary structure annotations + */ + Annotation ssE = new Annotation("","",'E',0); + Annotation ssH = new Annotation("","",'H',0); + Annotation ssS = new Annotation(".","",' ',0); + + Annotation[] anns1; + Annotation[] anns2; + + /* All secondary structure annotations are similar for each column + * Set up + * column 1 2 3 4 + * seq s1 F R K S + * ss E H S E + * + * seq s2 F S J L + * ss E H S E + */ + if(similar == "All Similar") { + + anns1 = new Annotation[] { ssE, ssH, ssS, ssE}; + anns2 = new Annotation[] { ssE, ssH, ssS, ssE}; + + } + + /* All secondary structure annotations are dissimilar for each column + * Set up + * column 1 2 3 4 + * seq s1 F R K S + * ss E E S E + * + * seq s2 F S J L + * ss H E E S + */ + else if(similar == "Not Similar") { + + anns1 = new Annotation[] { ssE, ssE, ssS, ssE}; + anns2 = new Annotation[] { ssH, ssH, ssE, ssS}; + + } + + /* Set up + * column 1 2 3 4 + * seq s1 F R K S + * ss H E S E + * + * seq s2 F S J L + * ss H E E S + */ + else { + + anns1 = new Annotation[] { ssH, ssE, ssS, ssE}; + anns2 = new Annotation[] { ssH, ssE, ssE, ssS}; + } + + + AlignmentAnnotation ann1 = new AlignmentAnnotation("Secondary Structure", + "Secondary Structure", anns1); + AlignmentAnnotation ann2 = new AlignmentAnnotation("Secondary Structure", + "Secondary Structure", anns2); + + s1.addAlignmentAnnotation(ann1); + s2.addAlignmentAnnotation(ann2); + + AlignmentI al = new Alignment(new SequenceI[] { s1, s2 }); + AlignFrame af = new AlignFrame(al, 300, 300); + af.setShowSeqFeatures(true); + af.getFeatureRenderer().findAllFeatures(true); + return af; + } + + + /** + * 
    +   * Set up
+   *   column      1 2 3 4 
+   *        seq s1 F R   S
+   *        	SS H E   S
+   *        
+   *        seq s2 F S J L
+   *        	ss H E E S
+   *
    + * + * @return + */ + protected AlignFrame setupAlignmentViewWithGap(String similar) + { + + SequenceI s1 = new Sequence("s1", "FR S"); + SequenceI s2 = new Sequence("s2", "FSJL"); + + s1.addSequenceFeature( + new SequenceFeature("chain", null, 1, 3, 0f, null)); + s1.addSequenceFeature( + new SequenceFeature("domain", null, 1, 3, 0f, null)); + s2.addSequenceFeature( + new SequenceFeature("chain", null, 1, 4, 0f, null)); + s2.addSequenceFeature( + new SequenceFeature("metal", null, 1, 4, 0f, null)); + s2.addSequenceFeature( + new SequenceFeature("Pfam", null, 1, 4, 0f, null)); + + + Annotation ssE = new Annotation("","",'E',0); + Annotation ssH = new Annotation("","",'H',0); + Annotation ssS = new Annotation(".","",' ',0); + + Annotation[] anns1; + Annotation[] anns2; + + anns1 = new Annotation[] { ssH, ssE, ssS}; + anns2 = new Annotation[] { ssH, ssE, ssE, ssS}; + + AlignmentAnnotation ann1 = new AlignmentAnnotation("Secondary Structure", + "Secondary Structure", anns1); + AlignmentAnnotation ann2 = new AlignmentAnnotation("Secondary Structure", + "Secondary Structure", anns2); + + s1.addAlignmentAnnotation(ann1); + s2.addAlignmentAnnotation(ann2); + + AlignmentI al = new Alignment(new SequenceI[] { s1, s2 }); + AlignFrame af = new AlignFrame(al, 300, 300); + af.setShowSeqFeatures(true); + af.getFeatureRenderer().findAllFeatures(true); + return af; + } + +} -- 1.7.10.2